Merge pull request #93 from simonsobs/fix-docs-params

adding bandshift params + fixing docs + other small fix

examples/mflike_example.yaml

@@ -3,7 +3,7 @@
 debug: True
 
 likelihood:
-  mflike.MFLike:
+  mflike.TTTEEE:
     input_file: LAT_simu_sacc_00044.fits
     cov_Bbl_file: data_sacc_w_covar_and_Bbl.fits
 

mflike/Foreground.yaml

@@ -60,4 +60,4 @@ params:
     latex: T_{\mathrm{dust},\mathrm{eff}}
   beta_d: #beta galactic dust
     value: 1.5
-    latex: \beta_\mathrm{dust}
+    latex: \beta_\mathrm{dust}

mflike/foreground.py

@@ -7,16 +7,26 @@
 If one wants to use this class as standalone, the ``bands`` dictionary is filled when initializing
 ``BandpowerForeground``.
 
-The values of the systematic parameters are set in ``MFLike.yaml``.  They have to be named as
-``cal/calT/calE/alpha`` + ``_`` + experiment_channel string (e.g. ``LAT_93/dr6_pa4_f150``).
+The default values of the systematic parameters are set in the ``TTTEEE/TEEE/TT/EE/TE/etc.yaml`` files.  They have to be named as ``cal/calT/calE/alpha`` + ``_`` + experiment_channel string (e.g. ``LAT_93/dr6_pa4_f150``).
+The default values of the foreground parameters are set in the ``fg_TT/TE/EE.yaml`` files.
+If you want to set different parameters settings, do that in the ``params`` block of the ``yaml`` file you will use for running (see the `examples/mflike_example.yaml <https://github.com/simonsobs/LAT_MFLike/blob/master/examples/mflike_example.yaml>`_).
+
+.. note::
+    Note that when you set different foregrounds/systematics parameters in the ``params`` block 
+    of your running ``yaml``, Cobaya will use the new parameters settings you indicated. If you
+    don't change a parameter setting in the ``params`` block, Cobaya will use its default stored
+    in the files mentioned above. Note that, in the ``.updated.yaml`` file generated by Cobaya, 
+    the ``mflike.BandpowerForeground`` theory block will have a ``params`` block with all the 
+    foreground parameters default settings which may be different from what you are defining in 
+    the general ``params`` block. 
 
 
 The bandpass shifts are applied within the ``_bandpass_construction`` function. There are two possibilities:
     * reading the passband :math:`\tau(\nu)` stored in a sacc file
       (which is the default now)
     * building the passbands :math:`\tau(\nu)`, either as Dirac delta or as top-hat
 
-For the second option, the ``top_hat_band`` dictionary in ``MFLike.yaml`` has to be filled with two keys:
+For the second option, the ``top_hat_band`` dictionary under the ``mflike.BandpowerForeground`` theory block has to be filled with two keys:
     * ``nsteps``: setting the number of frequencies used in the band integration
       (either 1 for a Dirac delta or > 1)
     * ``bandwidth``: setting the relative width :math:`\delta` of the band with respect to
@@ -32,10 +42,11 @@
 
 .. code-block:: yaml
 
-  top_hat_band:
-    nsteps: 1
-    bandwidth: 0
-
+  theory:
+    mflike.BandpowerForeground:
+      top_hat_band:
+        nsteps: 1
+        bandwidth: 0
 """
 
 import os

mflike/mflike.py

@@ -33,7 +33,7 @@
 
 If left ``null``, no systematic template is applied.
 
-The values of the systematic parameters are set in ``MFLike.yaml``.  They have to be named as
+The values of the systematic parameters are set in the ``TTTEEE/TTTE/TT/EE/TE/etc.yaml`` files corresponding to the classes that inherit the ``_MFLike`` one.  They have to be named as
 ``cal/calT/calE/alpha`` + ``_`` + experiment_channel string (e.g. ``LAT_93/dr6_pa4_f150``).
 """
 

mflike/mflike_common.yaml

@@ -19,3 +19,13 @@ alpha_LAT_145:
 alpha_LAT_225:
   value: 0 #deg
   latex: \alpha^{225}
+bandint_shift_LAT_93:
+  value: 0
+  latex: \Delta_{\rm band}^{93}
+bandint_shift_LAT_145:
+  value: 0
+  latex: \Delta_{\rm band}^{145}
+bandint_shift_LAT_225:
+  value: 0
+  latex: \Delta_{\rm band}^{225}
+